SAXSdb — 12np

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Secreted and transmembrane protein 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 29–137 Chain H； UniProt 29–137	Fragment：residues 1-109 of the mature protein	T-cell antigen CD7 × 2 （P09564）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M MgCl2, 0.1M Tris (pH=7.0), 6% w/v PEG8000	Resolution 2.40 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 29–137 Chain F； UniProt 29–137	Fragment：residues 1-109 of the mature protein	T-cell antigen CD7 × 2 （P09564）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M MgCl2, 0.1M Tris (pH=7.0), 6% w/v PEG8000	Resolution 2.40 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SCTM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–109； UniProt 29–137 Author chain B； PDBConstruct 1–109； UniProt 29–137 Author chain F； PDBConstruct 1–109； UniProt 29–137 Author chain H； PDBConstruct 1–109； UniProt 29–137

T-cell antigen CD7

Homo sapiens

UniProt P09564

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 26–145 Chain D； UniProt 26–145	Fragment：ectodomain	Secreted and transmembrane protein 1 × 2 （Q8WVN6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M MgCl2, 0.1M Tris (pH=7.0), 6% w/v PEG8000	Resolution 2.40 Å R-free 0.278
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 26–145 Chain G； UniProt 26–145	Fragment：ectodomain	Secreted and transmembrane protein 1 × 2 （Q8WVN6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M MgCl2, 0.1M Tris (pH=7.0), 6% w/v PEG8000	Resolution 2.40 Å R-free 0.278

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 12NP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
12HP Crystal structure of the CD7 ectodomain Deposited 2026-04-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 26–145（120 aa） Fragment：ectodomain Chain D 26–145（120 aa） Fragment：ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.7M NaH2PO4, 0.7M KH2PO4, 0.075M HEPES (pH=7.5), 25% glycerol	Resolution 2.00 Å R-free 0.268
12HP Crystal structure of the CD7 ectodomain Deposited 2026-04-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–145（120 aa） Fragment：ectodomain Chain B 26–145（120 aa） Fragment：ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.7M NaH2PO4, 0.7M KH2PO4, 0.075M HEPES (pH=7.5), 25% glycerol	Resolution 2.00 Å R-free 0.268
12HP Crystal structure of the CD7 ectodomain Deposited 2026-04-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 26–145（120 aa） Fragment：ectodomain Chain H 26–145（120 aa） Fragment：ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.7M NaH2PO4, 0.7M KH2PO4, 0.075M HEPES (pH=7.5), 25% glycerol	Resolution 2.00 Å R-free 0.268
12HP Crystal structure of the CD7 ectodomain Deposited 2026-04-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain F 26–145（120 aa） Fragment：ectodomain Chain G 26–145（120 aa） Fragment：ectodomain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.7M NaH2PO4, 0.7M KH2PO4, 0.075M HEPES (pH=7.5), 25% glycerol	Resolution 2.00 Å R-free 0.268

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD7_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–120； UniProt 26–145 Author chain D； PDBConstruct 1–120； UniProt 26–145 Author chain E； PDBConstruct 1–120； UniProt 26–145 Author chain G； PDBConstruct 1–120； UniProt 26–145

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	12np
Deposition date deposition_date	2026-04-13
最后修订 last_revision	2026-05-06
Structure title title	Crystal structure of the CD7 ectodomain bound to K12
Keywords keywords	Immunoglobulin, Immunoreceptor, surface receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.70 Å
Radius of gyration Rg (electron density) rg_electron	34.01 Å
Forward intensity I(0) i0	167621000.00
Molecular weight molecular_weight	97670.0 kDa
Excluded volume excluded_volume	119770 Å³
Envelope volume envelope_volume	161550 Å³
Hydration-shell volume shell_volume	40058 Å³
Envelope diameter envelope_diameter	118.9 Å
Shell Rg shell_rg	39.91 Å
Envelope Rg envelope_rg	33.52 Å
Shape Rg shape_rg	34.00 Å
Total Rg total_rg	34.50 Å
Total atoms total_atoms	6867
Residues n_residues	889
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	110.3 Å
Rg (real space) rg_real	34.59 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.6760e+08
I(0) uncertainty (real space) i0_real_error	2.7620e+06
Rg (reciprocal space) rg_reciprocal	34.66 Å
I(0) (reciprocal space) i0_reciprocal	167600000.0000
Solution quality estimate total_estimate	0.8971
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	48.0 Å
Skewness Skewness skewness	0.149
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20790000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.892

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Secreted and transmembrane protein 1
Molecular weight formula_weight	11977.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,F,H
Atom count atom_count	7077

QNEGWDSPICTEGVVSVSWGENTVMSCNISNAFSHVNIKLRAHGQESAIFNEVAPGYFSRDGWQLQVQGGVAQLVIKGARDSHAGLYMWHLVGHQRNNRQVTLEVSGAE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	T-cell antigen CD7
Molecular weight formula_weight	13162.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,E

AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

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8. Citations (1)

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Unit-cell length a length_a	49.681 Å
Unit-cell length b length_b	121.950 Å
Unit-cell length c length_c	88.871 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	44.990 Å
R factor r_factor	0.2431
R_work r_work	0.2414
R_free r_free	0.2781

fit	/app/data/saxs_computation/2n/12np/12np.fit
pddf	/app/data/pr_computation/2n/12np/12np.pr.out
profile	/app/data/saxs_computation/2n/12np/12np.dat

Crystal structure of the CD7 ectodomain bound to K12

1. Protein Identity and Related Structures Protein Identity & Related Structures

Secreted and transmembrane protein 1

State in the Current Structure

Other States of the Same Protein in the Database

T-cell antigen CD7

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)